MoBIE collection tables

MoBIE collection tables provide a convenient (human editable) way to specify correlative spatial data sets, including images, segmentations, segmentation annotations and annotated spots (e.g. useful for browsing gene locations in spatial transcriptomics data).

If you can’t wait to try this out, you may skip the explanations and immediately scroll to the below “Quick start” section.

Collection table specification

Each row specifies one dataset, which are be specified by a number of predefined columns. Please see here for a full specification of supported columns..

The only required column is called uri, which must contain a valid path to that dataset. This path can be local (File system) or in the cloud (S3 or HTTP).

In addition to the specified columns the table can contain arbitrary other columns that may contain interesting information about the respective data sets. Please make sure not to use column names that are part of the above specification.

Opening a collection table in Fiji/MoBIE

Within the Fiji menu select: Plugins > MoBIE > Open > Open Collection Table...

A user interface will pop up with the following fields:

• Table Uri: This is a mandatory field. Put here the location of a MoBIE collection table. This may be a path to a file on your computer or to a “cloud resource” such as an S3 object store or a GitHub URL. The collection table file can be provided in a number of formats, including EXCEL, CSV, TSV and Google Sheets. For Google Sheets simply copy and paste the link that shows in your browser or use the link that you obtain when using Google’s share table functionality.
• Data Root: This is a mandatory field.
  • PathsInTableAreAbsolute: Choose this if the uri column in the table contains absolute paths (for cloud resources that is always the case, for files on your computer it may be the case…)
  • UseTableFolder: Choose this option if the paths in the uri column are relative to the location of the collection table. This supports the scenario, where you have all your data organised within some folder structure and the collection table is at the root of this folder structure. This is a very useful setup because it allows you to move or copy the whole folder structure and opening the data via the collection table will still work.
  • UseBelowRootDataFolder: Choose this option if the paths in the uri column are relative to the location of the root data folder that you can specify below. This supports the scenario, where you have all your data organised within some folder structure and the collection table is, for some reason, not at the root of this folder structure.
• ( Data Root Folder ): This is an optional field. It is only considered if you chose UseBelowRootDataFolder above.
• Viewing mode: This is a mandatory field. It changes the browsing mode of BigDataViewer.
  • ThreeDimensional: Choose this is your data also contains 3-D images.
  • TwoDimensional: Choose this if all your data is 2-D (it will make you life easier, because you cannot get lost in 3-D while browsing your 2-D data).
• ( S3 Access Key )
• ( S3 Secret Key ) : These are optional fields. Fill those in if the uri column of the collection table points to data within a read protected S3 bucket.

Example collection tables

Below are some examples. Those are all Google sheets, so those links could be directly opened in the above described Open Collection Table... command.

• Correlative 2-D EM, fluorescence and 3-D tomography data
• Grid view of many OpenOrganelle EM volumes
• Grid view of a few OpenOrganelle EM volumes and organelle segmentations
• Large volume EM data, annotated cell segmentation, and a few annotated spots
• BioImage Archive multi-channel OME-Zarr
• ThinPlateSpline transformed EM volume

Quick start

Make sure to have MoBIE installed on your computer.

Within the Fiji menu select: Plugins > MoBIE > Open > Open Collection Table....

In the UI that pops up choose:

• Table Uri: https://docs.google.com/spreadsheets/d/1xZ4Zfpg0RUwhPZVCUrX_whB0QGztLN_VVNLx89_rZs4/edit?gid=0#gid=0
• Data Root: PathsInTableAreAbsolute
• ( Data Root Folder ): leave empty
• Viewing mode: ThreeDimensional
• ( S3 Access Key ) : leave empty
• ( S3 Secret Key ) : leave empty

Have fun browsing the data!

Note that you could use any of the URL of the above “Example collection tables” in the exact same way (just copy and paste the links into the Open Collection Table... command).

If you are unsure how to browse the data, this video should be helpful. More videos can be found in the MoBIE YouTube channel.

Troubleshooting